Re: [gmx-users] Binding energy of membrane protein to the membrane lipids

On 5/8/14, 3:38 PM, Victor Sojo wrote: Dear all, I'm trying to determine the binding energy of a membrane protein to the membrane. Ultimately I need to compare the binding energy of the same protein to two similar types of lipid, the hypothesis being that there should be a slight difference.

Re: [gmx-users] Binding energy of membrane protein to the membrane lipids

Dear all, I'm trying to determine the binding energy of a membrane protein to the membrane. Ultimately I need to compare the binding energy of the same protein to two similar types of lipid, the hypothesis being that there should be a slight difference. I considered two options: alchemical transf

Re: [gmx-users] Binding energy of membrane protein to the membrane lipids

Thanks so much, Justin! Your comments and paper are very helpful indeed. With "by eye" I meant I just need to know whether one is bigger than the other, but you're complete right: no need to speak in qualitative terms when I can quantitatively determine DeltaDeltaG. Thanks again! Victor Sojo

Re: [gmx-users] Binding energy of membrane protein to the membrane lipids

On 2/23/14, 11:54 AM, sojovictor wrote: Thanks, Justin! That's really helpful indeed. You are correct, I want to know what's the energy change in replacing one lipid with the other, hypothesising that going to the "wrong" lipid will imply an energetic cost. Via umbrella sampling, I would thus

Re: [gmx-users] Binding energy of membrane protein to the membrane lipids

Thanks, Justin! That's really helpful indeed. You are correct, I want to know what's the energy change in replacing one lipid with the other, hypothesising that going to the "wrong" lipid will imply an energetic cost. Via umbrella sampling, I would thus: 1) Set up a full system with protein, lip

Re: [gmx-users] Binding energy of membrane protein to the membrane lipids

On 2/23/14, 10:36 AM, sojovictor wrote: Dear all, I would like to find the difference in the energy of binding or insertion of a protein into two different types of phospholipid membranes (plus water and ions). i.e., my hypothesis is that the energy should be lower with one type of membrane th

[gmx-users] Binding energy of membrane protein to the membrane lipids

Dear all, I would like to find the difference in the energy of binding or insertion of a protein into two different types of phospholipid membranes (plus water and ions). i.e., my hypothesis is that the energy should be lower with one type of membrane than with the other. I have considered an alc